The ATP-binding cassette(ABC) transporters represent an important mechanism in transport of drugs and their metabolites. Substrate specificity screening of ABC transporters is of great interest to achieve a goal of rational drug molecular design. In this project, we have cloned human novel ABC transporters, such as ABCC11, ABCC12, and ABCC13, and also developed high-speed functional screening systems. By using the Chemical Fragmentation Codes, we have created a new quantitative structure-activity relationship(QSAR) analysis method to study the substrate specificity of ABC transporters. Analysis of the substrate specificity of ABCG2 led us to discovery of new camptothecin (CPT)-based drugs that may circumvent drug-resistance of human cancer. Based on our data, it is strongly suggested that hydrogen bond formation is critically involved in substrate recognition and/or transport processes of ABCG2. Furthermore, we performed structure-based molecular design to discover a highly selective catalytic site-directed inhibitor of Ser/Thr protein phosphatase 2B (PP2B/calcineurin). The cantharidin-based inhibitor, thus created, is very potent and specific to PP2B without inhibiting PP1 or PP2A. To our knowledge, this is the first highly selective catalytic-site-directed inhibitor of PP2B. In addition, we have designed novel protein kinase C(PKC) ligands that are as potent as TPA. By structural modifications, we have also succeeded in synthesizing PKC inhibitors that effectively inhibit the invasion of cancer cells.